#NEXUS [written Wed Apr 21 07:43:44 CEST 2010 by Mesquite version 2.72 (build 528) at pd954b983.dip.t-dialin.net/169.254.30.177] BEGIN TAXA; TITLE Untitled_Taxa_Block; DIMENSIONS NTAX=4; TAXLABELS taxonA taxonB taxonC taxonD ; END; BEGIN CHARACTERS; TITLE allBranches1.0_100_positions; [! Simulated Matrices on Current Tree: Matrix #1; Simulator: Evolve DNA Characters; most recent tree: allBranches1.0 [seed for matrix sim. 1271827960364] Evolve DNA Characters: Simulated evolution using model Jukes-Cantor with the following parameters: Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Probability Model for Simulation: Current model "Jukes-Cantor": Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Matrices: Character Matrices from file: Project of "fourTaxaBranchLengthDemoV2.nex" Tree of context: Tree(s) used from Tree Window 2 showing Stored Trees. Last tree used: allBranches1.0 [tree: ((1:1.0,2:1.0):0.5,(3:1.0,4:1.0):0.5):1.0;] ] DIMENSIONS NCHAR=100; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX taxonA ATCGCACAAACGAATATTGGATGGAGGCCGACAGTCCGATTTTTGAGGTCGATGCAGCGATTAAAGTCGTTTCAGTTCCTGTGGGGGAGTTCCAGTCCGT taxonB AGAGGTGTCACGCCAATTAGAGTCTAAGCGTCCAGTTCGTTCCGGGTTGCTATAGAAGCCTTATTGTCGCGTGTGTAAAACTAACTGAGTAACGCTATAT taxonC ATCTTCGCGCTGAGAGCTAGCACCTGAGAAATCTTGCGCGTTTGCAGCGAATTTATGAGCCCCTCCATGTCCTGGTGCCTGTGGTGCCAGCACAGCTGTC taxonD AGCCGGGCATCGAGCACCCCCCGATCTCACCGCCAGGGTTGGCCCGTCGCATTAAATAAATCCTCATAACCGATGCTCCTATACTAGTGATAAGTATCCT ; END; BEGIN CHARACTERS; TITLE allBranches0.1_100_positions; [! Simulated Matrices on Current Tree: Matrix #1; Simulator: Evolve DNA Characters; most recent tree: allBranches0.1 [seed for matrix sim. 1271828110756] Evolve DNA Characters: Simulated evolution using model Jukes-Cantor with the following parameters: Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Probability Model for Simulation: Current model "Jukes-Cantor": Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Matrices: Character Matrices from file: Project of "fourTaxaBranchLengthDemoV2.nex" Tree of context: Tree(s) used from Tree Window 2 showing Stored Trees. Last tree used: allBranches0.1 [tree: ((1:0.1,2:0.1):0.05,(3:0.1,4:0.1):0.05):0.1;] ] DIMENSIONS NCHAR=100; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX taxonA TCTTATTACATTGCAGTCACTGCTGTAATTATATGTCATGTCTCAGACGAACCAGCAAGTAATCTACTATACAGCAAAAATTATATTGTCCTGTCTAGAC taxonB TCTGATTACATTGCAGATTCTGCTCCGATTATATGTCATGTCTCAGAGGAACCTGTAAGTAAACTACTATATAGCAAAATTTATGTTGTGCTGTCTATAC taxonC TCTTATTACATTGTAGTCTCTGCTCTGACTATATGTCATGTCTCAGACGGACCAGTTCTTAAAGCACTATACAGCAAAATTTATATTGTCCTGTCTAGAC taxonD TCTTATTACATTGCAGTCTCTGCCCTGACTATATGTCATGTCTCAAACGAACCTGTACTTAAACGACTATACAGCAAAATTTATATTGTCCGGTATAAAC ; END; BEGIN CHARACTERS; TITLE threeTimesLongerInternalBranchExtBranch0.1_100_positions; [! Simulated Matrices on Current Tree: Matrix #1; Simulator: Evolve DNA Characters; most recent tree: threeTimesLongerInternalBranchExtBranch0.1 [seed for matrix sim. 1271828460361] Evolve DNA Characters: Simulated evolution using model Jukes-Cantor with the following parameters: Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Probability Model for Simulation: Current model "Jukes-Cantor": Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Matrices: Character Matrices from file: Project of "fourTaxaBranchLengthDemoV2.nex" Tree of context: Tree(s) used from Tree Window 2 showing Stored Trees. Last tree used: threeTimesLongerInternalBranchExtBranch0.1 [tree: ((1:0.1,2:0.1):0.05,(3:0.1,4:0.1):0.25):0.1;] ] DIMENSIONS NCHAR=100; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX taxonA TGACTGACCTGTCGAAGTTTTGAGATTGCACGCGCTCAGCGGGAGACATCTCAAGGGGACCCGCTAGGGCTACGTTCGGCTAGGATCCACATTAAGCCAT taxonB TAACTGACCTGTAGAAGAGTTGAGATTGGACGCGCTCAGCTGGAGACAACTCAAGGGCACCCGCTAGGGCTACGTTCGGCTAGGATCCATACTAAGCTAC taxonC TAACAGACCCGCCGTAGGTGTGACATGGCGGGCGATCCACGGGAGAAACCTCTAATGCACCAACTAGGGCTACGTAGGGCTAAGATACAAACAAAGCTCT taxonD TAGCAGACCTGACGGAGGTGTGCGATGGCGGGCGAGTCACTGGAGAAATCTCTAATGCACAAACTAGGGCTAAGTAGGGCTAGGATGCAAACAAAGCTAT ; END; BEGIN CHARACTERS; TITLE extBranches0.2IntBranch0.6_100_positions; [! Simulated Matrices on Current Tree: Matrix #1; Simulator: Evolve DNA Characters; most recent tree: extBranches0.2IntBranch0.6 [seed for matrix sim. 1271828548033] Evolve DNA Characters: Simulated evolution using model Jukes-Cantor with the following parameters: Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Probability Model for Simulation: Current model "Jukes-Cantor": Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Matrices: Character Matrices from file: Project of "fourTaxaBranchLengthDemoV2.nex" Tree of context: Tree(s) used from Tree Window 2 showing Stored Trees. Last tree used: extBranches0.2IntBranch0.6 [tree: ((1:0.2,2:0.2):0.1,(3:0.2,4:0.2):0.5):0.2;] ] DIMENSIONS NCHAR=100; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX taxonA ACCGCCCCGATCAGACGAATTTTAAAGCACTACTAGGCACTGTGAGTAACCACTTGTTGTCCTCCGATGACTGAAAGTTAGGTCACAGAACCCGTGATTA taxonB ACCGCCCCGATAAGACGAAGTTTAATTCGCCACTAGGCACTGTGAACAGCCAATCCTTGTCCTTCGATGAGTGAAAGTTAGTTCACTGAACCCGGCCTTA taxonC AGAGTCCTCGTAGGACGGCTTTAGTGTACGGTCAAGGCATTGTCTGAAGAGAACCTTTGTCTTACGATGAGTTTATGCTAGGCATAGGAACGGCCTGTTA taxonD AGAGTCCTGGAAGGAGGACTTGAGAGTAAGGTCCAGGCACTGTCAGAATTGAATAGTTGTCTTACGAAGATTAAAAGCCAGGCATAAGAACCCACTGTTA ; END; BEGIN CHARACTERS; TITLE ext0.8Int2.4_100_positions; [! Simulated Matrices on Current Tree: Matrix #1; Simulator: Evolve DNA Characters; most recent tree: ext0.8Int2.4 [seed for matrix sim. 1271828584723] Evolve DNA Characters: Simulated evolution using model Jukes-Cantor with the following parameters: Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Probability Model for Simulation: Current model "Jukes-Cantor": Root states model (Equal Frequencies): Equal Frequencies Equilibrium states model (Equal Frequencies): Equal Frequencies Character rates model (Equal Rates): Equal Rates Rate matrix model (Single Rate): single rate Stored Matrices: Character Matrices from file: Project of "fourTaxaBranchLengthDemoV2.nex" Tree of context: Tree(s) used from Tree Window 2 showing Stored Trees. Last tree used: ext0.8Int2.4 [tree: ((1:0.8,2:0.8):0.4,(3:0.8,4:0.8):2.0):0.8;] ] DIMENSIONS NCHAR=100; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX taxonA TGTCCTCCAATCACGCCAACATCCCACAGGACTCCGGCAATTCGATAGTTCGAGTAAAGGATCGGCGGACACGACTCAGTAGAACTAATTGTCCCTAAAC taxonB ATGCAAGAGCTCAACCTGTCCCAACCCGGGACTGCGGCCACCCAATACTAAGAAAATTTATGCAATATTGCAGATAGACAAACAAAAGATTTTGCAGGCG taxonC GGCCATAGAACAGGCAGTGATGTTGCTCTGATGTATCGGTGGAGGATGTCCGACTTCCAAGTGTCTTGATGAGTCTTATCATTGAGTGTAACCCGGTTCC taxonD GTCCACGAAGAACCGGGCACTGTTGTTTAGATCGACCGTCCGCACCCTTCCGGCTAGGTATCCTCTCTAGGACCGTTGCCCTGTCGAATATCGGTGGTCA ; END; BEGIN TREES; Title simulationTrees; LINK Taxa = Untitled_Taxa_Block; TRANSLATE 1 taxonA, 2 taxonB, 3 taxonC, 4 taxonD; TREE allBranches1.0 = ((1:1.0,2:1.0):0.5,(3:1.0,4:1.0):0.5):1.0; TREE allBranches0.1 = ((1:0.1,2:0.1):0.05,(3:0.1,4:0.1):0.05):0.1; TREE threeTimesLongerInternalBranchExtBranch0.1 = ((1:0.1,2:0.1):0.05,(3:0.1,4:0.1):0.25):0.1; TREE extBranches0.2IntBranch0.6 = ((1:0.2,2:0.2):0.1,(3:0.2,4:0.2):0.5):0.2; TREE ext0.8Int2.4 = ((1:0.8,2:0.8):0.4,(3:0.8,4:0.8):2.0):0.8; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = allBranches1.0_100_positions) = universal: 1 - 100; CODESET * UNTITLED (CHARACTERS = allBranches0.1_100_positions) = universal: 1 - 100; CODESET * UNTITLED (CHARACTERS = threeTimesLongerInternalBranchExtBranch0.1_100_positions) = universal: 1 - 100; CODESET * UNTITLED (CHARACTERS = extBranches0.2IntBranch0.6_100_positions) = universal: 1 - 100; CODESET * UNTITLED (CHARACTERS = ext0.8Int2.4_100_positions) = universal: 1 - 100; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = allBranches1.0_100_positions) = unord: 1 - 100; TYPESET * UNTITLED (CHARACTERS = allBranches0.1_100_positions) = unord: 1 - 100; TYPESET * UNTITLED (CHARACTERS = threeTimesLongerInternalBranchExtBranch0.1_100_positions) = unord: 1 - 100; TYPESET * UNTITLED (CHARACTERS = extBranches0.2IntBranch0.6_100_positions) = unord: 1 - 100; TYPESET * UNTITLED (CHARACTERS = ext0.8Int2.4_100_positions) = unord: 1 - 100; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = allBranches1.0_100_positions) = 'Jukes-Cantor': 1 - 100; ProbModelSet * UNTITLED (CHARACTERS = allBranches0.1_100_positions) = 'Jukes-Cantor': 1 - 100; ProbModelSet * UNTITLED (CHARACTERS = threeTimesLongerInternalBranchExtBranch0.1_100_positions) = 'Jukes-Cantor': 1 - 100; ProbModelSet * UNTITLED (CHARACTERS = extBranches0.2IntBranch0.6_100_positions) = 'Jukes-Cantor': 1 - 100; ProbModelSet * UNTITLED (CHARACTERS = ext0.8Int2.4_100_positions) = 'Jukes-Cantor': 1 - 100; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1271828624999; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2304910549831129530; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2360583090663266232; checksumv 0 2 3081782607 null getNumChars 100 numChars 100 getNumTaxa 4 numTaxa 4 short true bits 15 states 15 sumSquaresStatesOnly 8788.0 sumSquares 8788.0 NumFiles 1 NumMatrices 5; setID 1 2219722208120285442; checksumv 1 2 3371440578 null getNumChars 100 numChars 100 getNumTaxa 4 numTaxa 4 short true bits 15 states 15 sumSquaresStatesOnly 10231.0 sumSquares 10231.0 NumFiles 1 NumMatrices 5; setID 2 1755981188231063492; checksumv 2 2 3230035580 null getNumChars 100 numChars 100 getNumTaxa 4 numTaxa 4 short true bits 15 states 15 sumSquaresStatesOnly 7216.0 sumSquares 7216.0 NumFiles 1 NumMatrices 5; setID 3 7970514792810206263; checksumv 3 2 3956256744 null getNumChars 100 numChars 100 getNumTaxa 4 numTaxa 4 short true bits 15 states 15 sumSquaresStatesOnly 8374.0 sumSquares 8374.0 NumFiles 1 NumMatrices 5; setID 4 2874313267939747033; checksumv 4 2 2526454244 null getNumChars 100 numChars 100 getNumTaxa 4 numTaxa 4 short true bits 15 states 15 sumSquaresStatesOnly 8065.0 sumSquares 8065.0 NumFiles 1 NumMatrices 5; endTell; getWindow; tell It; suppress; setResourcesState false false 363; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1134 495; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #2304910549831129530 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #2304910549831129530; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #2304910549831129530 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1062.1271826551849.6657034781580429247; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 5; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; toggleShow consensusFrequency; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2360583090663266232 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #2219722208120285442 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #1755981188231063492 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #7970514792810206263 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #2874313267939747033 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 771 428; setLocation 40 55; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;